chr10:99804058:G>A Detail (hg38) (ABCC2)

Information

Genome

Assembly Position
hg19 chr10:101,563,815-101,563,815 View the variant detail on this assembly version.
hg38 chr10:99,804,058-99,804,058

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000647814.1:c.1249G>A ENST00000647814.1:p.Val417Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.113
ToMMo:0.129
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.085

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601107 OMIM
HGNC 53 HGNC
Ensembl ENSG00000023839 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv40386075 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-05-08 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-07-14 criteria provided, multiple submitters, no conflicts Dubin-Johnson syndrome germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2023-01-16 criteria provided, single submitter ABCC2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Adenocarcinoma of large intestine In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2... BeFree 16107775 Detail
0.001 Adenocarcinoma of large intestine In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2... BeFree 16107775 Detail
<0.001 Adenocarcinoma of large intestine In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2... BeFree 16107775 Detail
<0.001 Adenocarcinoma of large intestine In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2... BeFree 16107775 Detail
<0.001 Clear-cell metastatic renal cell carcinoma The DNA of all patients was genotyped for ABCB1 -2352G&gt;A, -692T&gt;C, 2677G&g... BeFree 16788565 Detail
<0.001 Clear-cell metastatic renal cell carcinoma The DNA of all patients was genotyped for ABCB1 -2352G&gt;A, -692T&gt;C, 2677G&g... BeFree 16788565 Detail
0.008 colorectal cancer The correlation of G1249A ABCC2 polymorphism with the development of colorectal ... BeFree 23232902 Detail
0.001 colorectal carcinoma The correlation of G1249A ABCC2 polymorphism with the development of colorectal ... BeFree 23232902 Detail
0.009 epilepsy The recessive model of MRP2 G1249A polymorphism decrease the risk of drug-resist... BeFree 25847339 Detail
0.009 epilepsy ABCC2 rs2273697 and rs3740066 polymorphisms and resistance to antiepileptic drug... BeFree 24624913 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000392.5(ABCC2):c.1249G>A (p.Val417Ile) AND not specified ClinVar Detail
NM_000392.5(ABCC2):c.1249G>A (p.Val417Ile) AND Dubin-Johnson syndrome ClinVar Detail
NM_000392.5(ABCC2):c.1249G>A (p.Val417Ile) AND not provided ClinVar Detail
NM_000392.5(ABCC2):c.1249G>A (p.Val417Ile) AND ABCC2-related disorder ClinVar Detail
In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2 were additionally e... DisGeNET Detail
In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2 were additionally e... DisGeNET Detail
In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2 were additionally e... DisGeNET Detail
In this study, 3 genotypes of MDR1, 4 genotypes of MRP1, and 6 genotypes of MRP2 were additionally e... DisGeNET Detail
The DNA of all patients was genotyped for ABCB1 -2352G&gt;A, -692T&gt;C, 2677G&gt;T/A (Ala893Ser/Thr... DisGeNET Detail
The DNA of all patients was genotyped for ABCB1 -2352G&gt;A, -692T&gt;C, 2677G&gt;T/A (Ala893Ser/Thr... DisGeNET Detail
The correlation of G1249A ABCC2 polymorphism with the development of colorectal cancer (CRC) and poo... DisGeNET Detail
The correlation of G1249A ABCC2 polymorphism with the development of colorectal cancer (CRC) and poo... DisGeNET Detail
The recessive model of MRP2 G1249A polymorphism decrease the risk of drug-resistant in Asian Epileps... DisGeNET Detail
ABCC2 rs2273697 and rs3740066 polymorphisms and resistance to antiepileptic drugs in Asia Pacific ep... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2273697 dbSNP
Genome
hg38
Position
chr10:99,804,058-99,804,058
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
52.36
Standard deviation of sample read depth (HGVD)
22.69
Number of reference allele (HGVD)
2142
Number of alternative allele (HGVD)
274
Allele Frequency (HGVD)
0.11341059602649006
Gene Symbol (HGVD)
ABCC2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs2273697
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1288
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2159
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
735
East Asian Heterozygous Counts (ExAC)
659
East Asian Homozygous Counts (ExAC)
38
East Asian Allele Frequency (ExAC)
0.08508914100486224
Chromosome Counts in All Race (ExAC)
121328
Allele Counts in All Race (ExAC)
23695
Heterozygous Counts in All Race (ExAC)
18771
Homozygous Counts in All Race (ExAC)
2462
Allele Frequency in All Race (ExAC)
0.19529704602400105
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